Kraut Daniel A, Sigala Paul A, Pybus Brandon, Liu Corey W, Ringe Dagmar, Petsko Gregory A, Herschlag Daniel
Department of Biochemistry, Stanford University, Stanford, California, United States of America.
PLoS Biol. 2006 Apr;4(4):e99. doi: 10.1371/journal.pbio.0040099. Epub 2006 Mar 28.
A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing pK(a) models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50-0.76 ppm/pK(a) unit, suggesting a bond shortening of 0.02 A/pK(a) unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (DeltaDeltaG = -0.2 kcal/mol/pK(a) unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (DeltaDeltaH = -2.0 kcal/mol/pK(a) unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of 300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
酶学领域一个长期存在的观点是,酶在静电和几何结构上与它们所催化反应的过渡态互补,且这种互补性有助于催化作用。然而,对这种贡献的实验评估一直很困难。我们系统地剖析了酮甾类异构酶中静电互补对催化作用的潜在贡献。酚盐是过渡态和反应中间体的类似物,在活性位点氧负离子洞中结合并接受两个氢键。具有恒定分子形状但pK(a)值不断增加的取代酚盐的结合,模拟了酶促反应过程中氧负离子洞中电荷的积累。随着电荷定位增加,参与氧负离子洞氢键的质子的核磁共振化学位移以每pK(a)单位增加0.50 - 0.76 ppm,这表明氢键缩短了每pK(a)单位0.02 Å。然而,一系列取代酚盐的结合亲和力几乎没有变化(ΔΔG = -0.2 kcal/mol/pK(a)单位)。尽管氢键缩短且结合焓有很大的有利变化(ΔΔH = -2.0 kcal/mol/pK(a)单位),电荷定位增加对亲和力的影响却很小。这种对结合亲和力的微弱依赖性表明,氧负离子洞中的静电互补对催化作用的贡献至多为300倍的适度贡献。我们提出,氧负离子洞氢键供体与过渡态氧负离子之间的几何互补提供了显著的催化贡献,并表明酮甾类异构酶与其他酶一样,是通过多种机制的适度贡献而非单一主导贡献的组合来实现其催化能力的。